Silver in PDB 6jr4: Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster

The structure of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster, PDB code: 6jr4 was solved by J.Kondo, C.Cerretani, H.Kanazawa, T.Vosch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.02 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	24.241, 33.849, 58.863, 90.00, 97.81, 90.00
R / Rfree (%)	12.6 / 14.6

The structure of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Silver atom in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (pdb code 6jr4). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 38 binding sites of Silver where determined in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster, PDB code: 6jr4:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 38 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:11.0 occ:1.00 N3 A:DC3 2.3 12.9 1.0 O2 A:DC1 2.4 11.7 1.0 AG A:AG105 2.7 11.1 1.0 AG A:AG111 2.7 11.3 1.0 AG A:AG102 2.8 10.8 1.0 AG A:AG110 2.8 12.1 1.0 O2 A:DC3 3.0 15.1 1.0 C2 A:DC3 3.0 15.1 1.0 N1 A:DA2 3.0 13.5 1.0 O6 A:DG9 3.2 11.8 1.0 C2 A:DA2 3.2 14.7 1.0 C4 A:DC3 3.2 17.3 1.0 N4 A:DC3 3.4 15.5 1.0 C2 A:DC1 3.4 12.5 1.0 C6 A:DA2 3.4 14.1 1.0 N3 A:DC4 3.6 14.8 1.0 N3 A:DC1 3.7 10.0 1.0 N3 A:DA2 3.7 13.0 1.0 C5 A:DA2 3.9 13.3 1.0 AG B:AG101 3.9 11.5 1.0 C4 A:DA2 4.0 13.2 1.0 N6 A:DA2 4.0 12.0 1.0 C6 A:DG9 4.1 13.9 1.0 N4 A:DC4 4.2 14.7 1.0 C4 A:DC4 4.4 15.1 1.0 N1 A:DC3 4.4 17.5 1.0 O2 A:DC4 4.5 13.6 1.0 C2 A:DC4 4.5 15.6 1.0 O2 B:DC3 4.5 12.9 1.0 N3 B:DC1 4.6 15.5 1.0 C5 A:DC3 4.6 15.6 1.0 N1 A:DC1 4.7 16.1 1.0 O2 B:DC1 4.7 17.1 1.0 N1 A:DG9 4.8 11.2 1.0 AG A:AG106 4.8 11.9 1.0 N7 A:DA2 4.9 14.2 1.0 N3 B:DC3 4.9 11.3 1.0 C5 A:DG9 4.9 14.2 1.0 N9 A:DA2 5.0 14.0 1.0 C6 A:DC3 5.0 18.4 1.0

Silver binding site 2 out of 38 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag102 b:10.8 occ:1.00 O6 A:DG9 2.4 11.8 1.0 N3 A:DC4 2.4 14.8 1.0 AG A:AG111 2.7 11.3 1.0 AG B:AG101 2.7 11.5 1.0 AG A:AG101 2.8 11.0 1.0 AG A:AG106 2.8 11.9 1.0 AG A:AG103 2.9 11.5 1.0 AG A:AG112 2.9 11.8 1.0 AG A:AG105 2.9 11.1 1.0 C2 A:DC4 3.1 15.6 1.0 O2 A:DC4 3.1 13.6 1.0 C4 A:DC4 3.3 15.1 1.0 C6 A:DG9 3.4 13.9 1.0 N4 A:DC4 3.5 14.7 1.0 N1 A:DG9 3.7 11.2 1.0 AG B:AG102 3.9 11.9 1.0 N3 A:DC3 3.9 12.9 1.0 AG A:AG110 3.9 12.1 1.0 N3 A:DC8 4.1 11.1 1.0 O2 A:DC3 4.1 15.1 1.0 C2 A:DC3 4.3 15.1 1.0 O2 B:DC4 4.3 12.1 1.0 O2 A:DC1 4.4 11.7 1.0 N1 A:DC4 4.4 18.0 1.0 C2 A:DC8 4.5 12.5 1.0 O2 A:DC8 4.5 14.0 1.0 N3 A:DC1 4.6 10.0 1.0 C5 A:DC4 4.6 16.6 1.0 C4 A:DC8 4.7 14.8 1.0 N1 B:DG9 4.7 13.2 1.0 O6 B:DG9 4.7 16.1 1.0 C5 A:DG9 4.7 14.2 1.0 C4 A:DC3 4.8 17.3 1.0 AG A:AG109 4.8 12.4 0.3 N4 A:DC8 4.8 17.1 1.0 N3 B:DC4 4.8 12.7 1.0 C2 A:DC1 4.9 12.5 1.0 N4 A:DC3 4.9 15.5 1.0

Silver binding site 3 out of 38 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag103 b:11.5 occ:1.00 N3 A:DC8 2.3 11.1 1.0 AG A:AG112 2.7 11.8 1.0 AG B:AG102 2.7 11.9 1.0 AG A:AG107 2.8 11.8 1.0 AG B:AG104 2.8 11.4 1.0 AG A:AG106 2.9 11.9 1.0 AG A:AG102 2.9 10.8 1.0 AG A:AG109 3.0 12.4 0.3 C2 A:DC8 3.1 12.5 1.0 AG A:AG104 3.1 11.0 1.0 O2 A:DC8 3.1 14.0 1.0 C4 A:DC8 3.2 14.8 1.0 N4 A:DC8 3.3 17.1 1.0 N3 A:DC4 3.6 14.8 1.0 C2 A:DC4 3.8 15.6 1.0 O2 A:DC4 3.9 13.6 1.0 AG B:AG101 4.1 11.5 1.0 O6 A:DG9 4.1 11.8 1.0 C4 A:DC4 4.2 15.1 1.0 N1 A:DC8 4.4 13.0 1.0 AG B:AG105 4.4 11.1 0.3 N7 A:DG7 4.5 13.2 1.0 AG B:AG103 4.5 11.8 1.0 C5 A:DC8 4.5 14.9 1.0 OP1 A:DA6 4.5 11.3 1.0 N1 A:DG9 4.5 11.2 1.0 N1 A:DC4 4.6 18.0 1.0 O2 B:DC8 4.6 13.5 1.0 N4 A:DC4 4.7 14.7 1.0 C6 A:DG9 4.7 13.9 1.0 N3 B:DC8 4.9 13.2 1.0 AG A:AG111 4.9 11.3 1.0 C5 A:DC4 4.9 16.6 1.0 C6 A:DC8 5.0 12.0 1.0

Silver binding site 4 out of 38 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag104 b:11.0 occ:1.00 N7 A:DG7 2.3 13.2 1.0 OP1 A:DA6 2.4 11.3 1.0 AG A:AG107 2.7 11.8 1.0 AG B:AG104 2.8 11.4 1.0 AG A:AG113 2.8 12.0 1.0 AG A:AG108 2.8 11.5 1.0 N3 A:DC8 3.0 11.1 1.0 AG A:AG103 3.1 11.5 1.0 C8 A:DG7 3.3 15.7 1.0 P A:DA6 3.3 15.0 1.0 C5 A:DG7 3.4 12.6 1.0 OP2 A:DA6 3.4 14.7 1.0 C2 A:DC8 3.5 12.5 1.0 O2 A:DC8 3.6 14.0 1.0 O6 A:DG7 3.6 10.2 1.0 C4 A:DC8 3.7 14.8 1.0 AG B:AG103 3.8 11.8 1.0 C6 A:DG7 3.9 11.2 1.0 N4 A:DC8 3.9 17.1 1.0 AG A:AG109 3.9 12.4 0.3 N7 A:DA6 4.1 12.8 1.0 C8 A:DA6 4.1 13.8 1.0 O6 B:DG7 4.1 14.9 1.0 O3' A:DT5 4.4 15.7 1.0 N9 A:DG7 4.5 14.6 1.0 O5' A:DA6 4.5 19.8 1.0 AG B:AG102 4.5 11.9 1.0 O A:HOH210 4.5 13.8 1.0 N1 A:DC8 4.6 13.0 1.0 C4 A:DG7 4.6 14.4 1.0 C5 A:DC8 4.7 14.9 1.0 C3' A:DT5 4.9 14.9 1.0 N7 B:DA6 4.9 16.2 1.0

Silver binding site 5 out of 38 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag105 b:11.1 occ:1.00 N3 A:DC1 2.3 10.0 1.0 O2 B:DC4 2.5 12.1 1.0 AG A:AG101 2.7 11.0 1.0 AG B:AG101 2.7 11.5 1.0 AG A:AG110 2.8 12.1 1.0 O2 B:DC3 2.8 12.9 1.0 AG A:AG102 2.9 10.8 1.0 C2 A:DC1 3.0 12.5 1.0 O2 A:DC1 3.1 11.7 1.0 AG A:AG106 3.1 11.9 1.0 O6 A:DG9 3.2 11.8 1.0 C4 A:DC1 3.2 11.1 1.0 N1 A:DG9 3.3 11.2 1.0 C2 B:DC4 3.3 13.9 1.0 N4 A:DC1 3.4 12.9 1.0 C6 A:DG9 3.4 13.9 1.0 N3 B:DC4 3.5 12.7 1.0 C2 B:DC3 3.6 14.9 1.0 N3 B:DC3 3.8 11.3 1.0 AG A:AG111 3.9 11.3 1.0 N6 A:DA2 4.0 12.0 1.0 N1 A:DA2 4.1 13.5 1.0 C2 A:DG9 4.2 13.0 1.0 C6 A:DA2 4.3 14.1 1.0 N1 A:DC1 4.4 16.1 1.0 C5 A:DG9 4.5 14.2 1.0 N1 B:DC4 4.5 13.1 1.0 C5 A:DC1 4.6 13.8 1.0 N2 A:DG9 4.6 15.2 1.0 N1 B:DC3 4.7 14.6 1.0 C4 B:DC4 4.8 15.9 1.0 AG B:AG102 4.8 11.9 1.0 N3 A:DC3 4.8 12.9 1.0 AG A:AG112 5.0 11.8 1.0 C6 A:DC1 5.0 14.3 1.0

Silver binding site 6 out of 38 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 6 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag106 b:11.9 occ:1.00 N1 A:DG9 2.3 11.2 1.0 O2 B:DC4 2.6 12.1 1.0 AG B:AG102 2.7 11.9 1.0 AG B:AG105 2.7 11.1 0.3 AG A:AG102 2.8 10.8 1.0 AG A:AG103 2.9 11.5 1.0 AG B:AG101 3.1 11.5 1.0 O6 A:DG9 3.1 11.8 1.0 AG A:AG105 3.1 11.1 1.0 C6 A:DG9 3.1 13.9 1.0 AG A:AG107 3.2 11.8 1.0 C2 A:DG9 3.3 13.0 1.0 N2 A:DG9 3.3 15.2 1.0 O2 A:DC8 3.4 14.0 1.0 C2 B:DC4 3.4 13.9 1.0 N3 B:DC4 3.8 12.7 1.0 AG A:AG112 4.0 11.8 1.0 C2 A:DC8 4.1 12.5 1.0 N3 A:DC8 4.2 11.1 1.0 N3 A:DC1 4.4 10.0 1.0 N1 B:DC4 4.4 13.1 1.0 N4 A:DC1 4.4 12.9 1.0 C5 A:DG9 4.5 14.2 1.0 N3 A:DG9 4.5 12.9 1.0 C1' B:DC4 4.7 12.9 1.0 N3 B:DC8 4.8 13.2 1.0 AG A:AG101 4.8 11.0 1.0 N3 A:DC4 4.8 14.8 1.0 AG B:AG104 4.8 11.4 1.0 N4 B:DC8 4.9 16.5 1.0 C4 A:DC1 4.9 11.1 1.0 C4 A:DG9 4.9 11.3 1.0

Silver binding site 7 out of 38 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 7 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag107 b:11.8 occ:1.00 AG B:AG105 2.6 11.1 0.3 O6 A:DG7 2.7 10.2 1.0 AG A:AG104 2.7 11.0 1.0 AG A:AG108 2.8 11.5 1.0 AG B:AG103 2.8 11.8 1.0 AG A:AG103 2.8 11.5 1.0 O2 A:DC8 2.9 14.0 1.0 AG B:AG102 2.9 11.9 1.0 AG A:AG106 3.2 11.9 1.0 AG B:AG104 3.2 11.4 1.0 C6 A:DG7 3.6 11.2 1.0 C2 A:DC8 3.7 12.5 1.0 N3 A:DC8 3.7 11.1 1.0 OP1 B:DA6 3.8 13.4 1.0 N7 A:DG7 3.8 13.2 1.0 C5 A:DG7 4.0 12.6 1.0 AG A:AG113 4.0 12.0 1.0 OP2 B:DA6 4.3 12.1 1.0 N3 B:DC8 4.4 13.2 1.0 P B:DA6 4.4 12.2 1.0 O3' B:DT5 4.7 14.6 1.0 N1 A:DG9 4.7 11.2 1.0 N1 A:DG7 4.8 14.4 1.0 N4 B:DC8 4.8 16.5 1.0 N2 A:DG9 4.8 15.2 1.0 AG A:AG112 4.9 11.8 1.0 C2' B:DT5 4.9 15.3 1.0 N7 A:DA6 4.9 12.8 1.0 N1 A:DC8 4.9 13.0 1.0 C4 A:DC8 5.0 14.8 1.0

Silver binding site 8 out of 38 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 8 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag108 b:11.5 occ:1.00 OP2 B:DA6 2.3 12.1 1.0 N7 A:DA6 2.4 12.8 1.0 O6 A:DG7 2.4 10.2 1.0 AG A:AG113 2.7 12.0 1.0 AG A:AG107 2.8 11.8 1.0 AG B:AG103 2.8 11.8 1.0 AG A:AG104 2.8 11.0 1.0 C6 A:DG7 3.2 11.2 1.0 C8 A:DA6 3.2 13.8 1.0 P B:DA6 3.3 12.2 1.0 C5 A:DA6 3.4 13.9 1.0 N7 A:DG7 3.6 13.2 1.0 OP1 B:DA6 3.6 13.4 1.0 N6 A:DA6 3.7 12.1 1.0 C5 A:DG7 3.7 12.6 1.0 N7 B:DA6 3.7 16.2 1.0 C8 B:DA6 3.7 17.9 1.0 O3' B:DT5 3.9 14.6 1.0 C6 A:DA6 4.0 12.9 1.0 AG B:AG104 4.1 11.4 1.0 OP2 A:DA6 4.2 14.7 1.0 N1 A:DG7 4.4 14.4 1.0 N9 A:DA6 4.4 13.5 1.0 C4 A:DA6 4.5 16.0 1.0 AG B:AG105 4.6 11.1 0.3 N7 B:DG7 4.6 18.4 1.0 O5' B:DA6 4.7 14.5 1.0 O2 A:DC8 4.7 14.0 1.0 OP1 A:DA6 4.8 11.3 1.0 C8 A:DG7 4.8 15.7 1.0 O6 B:DG7 4.9 14.9 1.0 C3' B:DT5 5.0 13.0 1.0 C4 A:DG7 5.0 14.4 1.0

Silver binding site 9 out of 38 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 9 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag109 b:12.4 occ:0.33 AG B:AG104 2.6 11.4 1.0 AG A:AG112 2.7 11.8 1.0 AG A:AG103 3.0 11.5 1.0 N6 B:DA10 3.0 19.2 1.0 N4 A:DC8 3.2 17.1 1.0 O2 A:DC4 3.4 13.6 1.0 N2 B:DG9 3.5 17.8 1.0 C2' A:DT5 3.6 15.3 1.0 C1' A:DC4 3.7 22.8 1.0 C2 A:DC4 3.7 15.6 1.0 N1 A:DC4 3.8 18.0 1.0 OP1 A:DA6 3.8 11.3 1.0 O6 B:DG7 3.8 14.9 1.0 C3' A:DT5 3.8 14.9 1.0 O2 B:DC8 3.9 13.5 1.0 AG A:AG104 3.9 11.0 1.0 N1 B:DG9 4.0 13.2 1.0 N3 A:DC8 4.1 11.1 1.0 C4 A:DC8 4.2 14.8 1.0 C2 B:DG9 4.2 19.3 1.0 C2' A:DC4 4.2 21.9 1.0 C6 B:DA10 4.3 19.4 1.0 AG B:AG102 4.3 11.9 1.0 O3' A:DT5 4.4 15.7 1.0 N3 A:DC4 4.5 14.8 1.0 N7 B:DA10 4.6 22.3 1.0 P A:DA6 4.7 15.0 1.0 C6 A:DC4 4.7 24.0 1.0 C6 B:DG7 4.8 18.4 1.0 AG A:AG102 4.8 10.8 1.0 AG A:AG113 4.8 12.0 1.0 C5 B:DA10 4.8 22.4 1.0 O4' A:DC4 4.9 21.9 1.0

Silver binding site 10 out of 38 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 10 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag110 b:12.1 occ:1.00 N3 B:DC3 2.2 11.3 1.0 N1 A:DA2 2.5 13.5 1.0 O2 B:DC1 2.6 17.1 1.0 AG A:AG111 2.7 11.3 1.0 AG A:AG105 2.8 11.1 1.0 AG A:AG101 2.8 11.0 1.0 AG B:AG101 2.8 11.5 1.0 O2 B:DC3 3.0 12.9 1.0 C2 B:DC3 3.0 14.9 1.0 C2 A:DA2 3.2 14.7 1.0 C4 B:DC3 3.3 13.9 1.0 C6 A:DA2 3.4 14.1 1.0 N4 B:DC3 3.5 14.7 1.0 C2 B:DC1 3.5 15.8 1.0 N6 A:DA2 3.6 12.0 1.0 N3 B:DC1 3.7 15.5 1.0 O6 B:DG9 3.9 16.1 1.0 AG A:AG102 3.9 10.8 1.0 N3 B:DC4 4.0 12.7 1.0 O2 A:DC1 4.3 11.7 1.0 N1 B:DC3 4.3 14.6 1.0 N3 A:DA2 4.4 13.0 1.0 N3 A:DC1 4.5 10.0 1.0 O2 B:DC4 4.5 12.1 1.0 C6 B:DG9 4.5 16.2 1.0 O2 A:DC3 4.5 15.1 1.0 C5 A:DA2 4.6 13.3 1.0 C5 B:DC3 4.6 19.9 1.0 C2 B:DC4 4.6 13.9 1.0 N4 B:DC4 4.7 15.1 1.0 C2 A:DC1 4.8 12.5 1.0 C4 B:DC4 4.8 15.9 1.0 N1 B:DC1 4.8 19.8 1.0 N3 A:DC3 4.9 12.9 1.0 AG A:AG112 4.9 11.8 1.0 C4 A:DA2 4.9 13.2 1.0 N1 B:DG9 4.9 13.2 1.0 C6 B:DC3 5.0 16.0 1.0

C.Cerretani, H.Kanazawa, T.Vosch, J.Kondo. Crystal Structure of A Nir-Emitting Dna-Stabilized AG16NANOCLUSTER. Angew.Chem.Int.Ed.Engl. V. 58 17153 2019.
ISSN: ESSN 1521-3773
PubMed: 31411360
DOI: 10.1002/ANIE.201906766